merge with devel

.Rbuildignore

@@ -1,2 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.travis.yml
+appveyor.yml
+^\.git\*
+^\.gitignore

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: OmicsMarkeR
 Title: Classification and Feature Selection for 'Omics' Datasets
 Description: Tools for classification and feature selection for 'omics' level
-    datasets.  It is a tool to provide multiple multivariate classification 
-    and feature selection techniques complete with multiple stability metrics 
+    datasets.  It is a tool to provide multiple multivariate classification
+    and feature selection techniques complete with multiple stability metrics
     and aggregation techniques.  It is primarily designed for analysis of
     metabolomics datasets but potentially extendable to proteomics and
     transcriptomics applications.
@@ -11,9 +11,12 @@ Version: 1.7.1
 Author: Charles E. Determan Jr. <cdetermanjr@gmail.com>
 Maintainer: Charles E. Determan Jr. <cdetermanjr@gmail.com>
 VignetteBuilder: knitr
-Depends: 
+Depends:
     R (>= 3.2.0)
-Imports: 
+Imports:
+    graphics,
+    stats,
+    utils,
     plyr (>= 1.8),
     data.table (>= 1.9.4),
     caret (>= 6.0-37),
@@ -36,5 +39,8 @@ BugReports: http://github.com/cdeterman/OmicsMarkeR/issues/new
 biocViews: Metabolomics, Classification, FeatureExtraction
 Packaged: 2015-07-27 08:27:19 UTC
 Repository: Bioconductor
-Suggests: testthat, BiocStyle, knitr
-
+Suggests:
+    testthat,
+    BiocStyle,
+    knitr
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(RPT)
 export(aggregation)
@@ -36,9 +36,12 @@ import(e1071)
 import(foreach)
 import(gbm)
 import(glmnet)
+import(graphics)
 import(pamr)
 import(plyr)
 import(randomForest)
+import(stats)
+import(utils)
 importFrom(caret,best)
 importFrom(caret,confusionMatrix)
 importFrom(caret,createDataPartition)

R/aggregation.R

@@ -2,6 +2,9 @@
 ### Aggregation Methods ###
 ###########################
 
+
+#' @import utils
+
 ## Notation
 # s = selected number of top ranking features
 # r = feature rank

R/data.generation.R

@@ -2,6 +2,7 @@
 ### Simulated Metabolomics Data ###
 ###################################
 
+#' @import stats
 plus_minus <- function(beta){
     inv <-rbinom(beta,1,0.5)
     inv <-ifelse(inv==0,-1,1)

R/perm.class.R

@@ -1,5 +1,6 @@
 # Performance Permutation
 
+#' @import graphics
 # declare global variables (i.e. the foreach iterators)
 globalVariables(c('p', 'fold'))
 
@@ -210,7 +211,7 @@ perm.class <-
     {
       #stop("prediction results failed")
       stop(paste("prediction results failed on", 
-                 method, outIndex, sep = " "))
+                 method, " fold: ", fold, sep = " "))
     }
 
     # what should it do if createModel fails???

R/stability.R

@@ -289,6 +289,8 @@ kuncheva <- function(x,
 #' approach.
 #' @param features A matrix of selected features
 #' @param stability.metric string indicating the type of stability metric.
+#' @param nc Optional argument to be used with 'kuncheva' stability.  Refers
+#' to the number of variables in original data.
 #' Available options are \code{"jaccard"} (Jaccard Index/Tanimoto Distance),
 #'  \code{"sorensen"} (Dice-Sorensen's Index), \code{"ochiai"} (Ochiai's Index),
 #'  \code{"pof"} (Percent of Overlapping Features), \code{"kuncheva"}